Kathryn the Borg Queen
by NarcissaMalfoy1119
Summary: What would have happened if Chakotay came home early before Kathryn was killed? Would he be able to save her from the Borg? Let's find out ;D
1. The Return Home

_**What would have happened if Chakotay returned back from his mission early before Kathryn was killed? Let's find out ;D **_

_**~Cissa**_

* * *

It had been a month since Chakotay and the Voyager crew had left on their mission. One month since he had last seen Kathryn. Once month since he had held her in his arms and heard her say she loved him. Now he was coming home and they would be able to start their new lives together. Where it led them, he didn't know. However, he was optimistic about the future and couldn't wait to share it with her. They docked at Deep Space One, right above earth. As Chakotay prepared to exit the ship his heart began beating rapidly. He was about to see Kathryn again. For weeks her face had never left his thoughts, she was always on his mind, and now he would finally be seeing her again. He took a deep breath as the transporter engaged and he was beamed to Starfleet Headquarters. As he materialized he was surprised that, instead of the petit, auburn haired beauty he had expected he was instead met by a tall, lanky, blond he had never thought to see again.

"Seven…what are you doing here? Where's Kath…the admiral?" he asked.

"Chakotay, something has happened. The admiral is gone," was all she said in reply, her face showing no sign of emotion. The words hit him like a ton of bricks, knocking his breath away. He couldn't breathe, he couldn't think. The only thing that ran through his mind was It can't be true. It just can't be. Not Kathryn.

"What…happened?" he finally managed to choke out after several seconds of stunned silence.

"She was assimilated by the Borg," Seven replied curtly.

"But…how? When?"

"May we go somewhere more private Captain? I'll explain everything."

"Of course. We can beam back to my ready room."

…

"About one week after you had left a Borg cube was spotted on our radar. It appeared to be dormant. The admiral wanted to explore it, to gather proof that there was no need for Voyager to be sent back into the Delta Quadrant."

"But why didn't you stop her!" he said, trying to contain his anger, "Why did you let her go! You, of all people, Seven! You knew it was dangerous!"

"I tried Captain. But you know the Admiral. She's very…"

"Stubborn," he finished for her with a sigh. "I'm sorry Seven. You might was well have stopped a river from flowing."

"It's quite alright Captain. Shall I continue?"

"Yes. Please do."

"Well, when she entered the cube it activated and she was assimilated immediately."

"And where is the cube now? What had been done to save her?"

"The cube is still in this Quadrant. We have sent several squads of trained tactical officers into the cube, but it's no use. She assimilated them all."

"She...?" he asked, confused.

"The admiral has been made the new Borg Queen."

…

"I've got to find her!" he said to Admiral Paris a few hours later.

"I understand your concern Captain, but we've done everything we can. I'm not risking any more of my trained officers on this suicide mission. We need to shut the cube down."

"And kill her in the process! You can't do that!"

"What other choice do I have Captain? You know she wouldn't want to live like this."

"Let me go by myself."

"You'd be going to your death captain. I can't allow that."

"I would rather die than live without her," he burst out, blushing when he realized what he had just said.

"Ah," said Admiral Paris knowingly with a sad smile, "I see how it is. I always thought something like this had happened out there. Tom told me…but that's not important right now."

"What did Tom tell you?" Chakotay demanded, curious.

"Only that you and Admiral Janeway were very close."

"And…" Chakotay prompted, sensing there was more.

"And that everyone on the ship could see how much you two loved each other…except for the both of you."

Chakotay just sighed, "Was it really that obvious?"

"According to Tom not even a Gorkon with a bad sense of direction could have missed it."

Groaning, Chakotay placed his hands in his head, looking up a few seconds later. "Please Sir, you have to let me find her. You have to let me try."

Standing up Admiral Paris put his hand on Chakotay's shoulder and looked into his eyes, "Permission granted."

…

The next day Chakotay was ready. "You have 24 hours Captain. After that, I have to shut the cube down," Admiral Paris told him as he was about to board Voyager.

"I understand sir. Thank you."

"And take care of my son and Daughter-in-law."

"I always will," Chakotay said with a smile. Walking onto the bridge a few minutes later he gave the order, "Tom, set a course for the Borg Cube. Engage."

…

Chakotay had never been on a Borg cube before. It had always been Kathryn who had gone on these missions, leaving him in charge of Voyager. It was eerie to say the least, the green glow giving a gloomy feel to his surroundings. As he walked along the corridors he was surprised to see no drones anywhere. Were they all with her? As he rounded a corner however he found himself surrounded by ten of them. Grabbing his phaser he got off a few shots before they adapted. As one grabbed him he elbowed it in the ribs, sending it backwards. Another came and grabbed his arms, but he disabled it with a swift kick. Soon he was overwhelmed however as two Borg grabbed his arms and other pointed a phaser in his back. Preparing himself for assimilation, he was surprised to not feel the tubules inject the nanoprobes into his neck. Instead the Borg with the phaser prodded him forward and they forced him to walk down the hall. Soon they entered a chamber with one lone regeneration alcove. On the opposite side of the room was the figure of a woman he knew all too well…


	2. Queen Kathryn

"Kathryn?" Chakotay asked, approaching the petite figure that had his back turned to him. When she turned around he could see that it was indeed Kathryn, but she was warped almost beyond recognition. Beneath the Borg exterior was just a shadow of the woman he loved. Her long auburn hair was gone, completely shaved off her head. Instead of a Starfleet uniform, her slender frame was covered in a black, mechanical cat suit. Her once warm and beautiful smile turned into a leer as she turned around and saw him. The only things remotely recognizable were her eyes…those beautiful grey eyes of hers were still there, though they were now turned hard and had lost all their usual warmth.

"Your precious Kathryn is gone!" Even her voice was different. The grating, nasally voice had turned smooth and seductive. Personally, Chakotay preferred her original voice. The Borg Kathryn slowly walked over to him, looking into his eyes with hers.

"I don't believe that," he replied, calmly.

"Why do you doubt your senses? She is gone and is never coming back! But why mourn for her?" she countered as she walked around him, dragging her hand seductively around his shoulders. "She was weak…flawed…imperfect."

"Kathryn is perfect to me!" he said, his voice rising with emotion for the first time, "She is beautiful, kind, compassionate, brave, everything you can never hope to be!" The Borg Kathryn's laugh rang out hard and cold through the chamber.

"Kindness…compassion...weaknesses you humans only perceive as strengths."

"They are what make us unique!"

"Uniqueness is irrelevant!"

Several seconds passed as they stared at each other. Chakotay's chest heaved with emotion while the Borg Kathryn's eyes shone with deep loathing.

"If Kathryn's gone, then why did you bring me here?" he finally managed to ask, "Why didn't you assimilate me when I beamed aboard your ship."

"One word," she said, giving him an arch look almost akin to the ones Kathryn used to give him, "curiosity." She turned around and began walking away from him, back towards her alcove. "We wanted to see what you would say-what you would do-when you found your beloved Kathryn gone and us in her place. We knew you two shared a…special…bond and wanted to test it."

"Well, you've got your results. Why don't you just assimilate me now and get it over with."

"Oh no my dear Commander, that would be too easy. We want to watch you suffer – suffer in the knowledge that your beloved is gone forever! That she will never again be by your side. That would be a fate far worse for you than assimilation. That is the experiment."

"But Kathryn isn't gone."

"How many times must we tell you? Kathryn Janeway is gone and she is never coming back to you!" she said, walking back over to him.

"And I don't believe that!" Chakotay said, standing up straight and meeting her gaze, "Kathryn is stronger than you'll ever be and she will never stop fighting you!" Reaching up he cupped the Borg Kathryn's face in his hand and looked into her eyes. "Please Kathryn. Don't leave me alone. I need you…" he whispered. The Borg jerked back and stared at him, surprise on her face. Suddenly her expression changed – her eyes widened like a lost puppy and her face lost the coldness of the Borg. "Chakotay! Help me!" she said in her normal, raspy voice.

"Kathryn! Hang in there! You can beat her!" he said taking her hand and giving it a squeeze. As suddenly as she had come she was gone again and the Queen was back, yanking her hand out of his with a snarl and throwing him crashing against the wall. He hit his head and blood trickled down his cheek. He tried to move and moaned, realizing his ribs were broken, or at least cracked.

"Chakotay!" Kathryn was back and she ran over to help him. Cupping his face in her hand, she asked, "Are you alright?"

"I'm…fine…" he groaned, "You?"

"She's strong Chakotay," she said, grabbing his hand, "I don't know if I can beat her."

"Yes you can Kathryn! Don't give in! Stay with me! You can do this!"

"I'm...trying…too…hard," Kathryn spoke with a lot more effort now, straining every word. She shook her head fiercely and the Borg was back. She stood up and stared down at him, crumpled and broken on the ground. "Pathetic human; so frail…so weak. We are the Borg. We are perfection."

"I see nothing…perfect…about…you!" he managed to say, every word painful on his broken ribs. For a second he saw the old Kathryn flicker across the Borg's eyes before she disappeared again. This sight gave him renewed strength. He pushed himself off the ground and stood up, suppressing a moan as a sharp pain shot through his sides. "Kathryn is perfect, and she's still in their fighting," he said, grabbing onto her shoulders, "come on Kathryn! You can do it!" The Borg threw him back again, sending him flying into the alcove, this time he heard a snap and felt his arm shatter underneath him as he cried out in pain. She walked over and glared down at him, "Perhaps I will terminate you and save you from your pathetic existence. You'll do no good to me as a drone now, and your denial of the evidence before you makes my experiment irrelevant." Her mechanical arm morphed into a phaser and he closed his eyes as she pointed it as his chest. "I love you Kathryn," he whispered softly. Suddenly he heard Kathryn's normal voice call out "NO!" He opened his eyes just as the Borg arm jerked up and the phaser blast shot through the ceiling.

Soon the slim, petite figure was kneeling next to him again. He moaned as she drew him to her, laying his head on her lap. Caressing his cheek softly with her fingers she whispered, "I love you too Chakotay" before he slipped into oblivion and the darkness consumed him.


	3. Resolutions

A bright light shone in his eyes as Chakotay slowly slipped back into consciousness. He blinked several times before attempting to sit up, gasping as pain shot through his ribs. A small, gentle hand placed itself on his chest, easing him down to the bed. He realized he must be in Voyager's sickbay. "Rest Chakotay," said a familiar voice.

"Kathryn," he said, hardly daring to believe his eyes. Yet there she sat next to him: her grey eyes back to normal, her petite figure dressed in Sickbay clothes, her warm smile radiating down to him, and her small hand resting firmly in his.

"I'm here Chakotay," she said, cupping his face with her free hand, "You saved me."

"Your hair," he said, running his hand through the short pixie cut she now wore.

"The Dr. regrew as much as he could with the regenerator. However, I have to wait for time to do the rest." She bit her lip, her eyes giving him an apprehensive look.

"What is it Kathryn?" he said, giving her hand a squeeze.

"Do you like it?" she asked in a small voice, clearly worried. Laughing, he reached up and tousled her hair, causing her to smile; "You've never looked more beautiful."

They stared at each other for several moments, the happiness and joy shining in both their eyes.

"I suppose you want to know what happened." Kathryn asked him, suddenly breaking the silence.

"Not right now," he said, slowly propping himself up on one arm and gingerly pulling her toward him with the other. Their lips met, softly at first, but the kiss soon became hungrier and more passionate. After several seconds they broke apart.

"Where's the Dr?" he asked her, looking around expecting to see the hologram hovering nearby.

"I deactivated him," Kathryn replied with a sly smile, "I wanted to be the one to care for you."

"There's no one I would rather have," he said, kissing her again.

"Speaking of which, I should probably run some more scans," she said, getting up and grabbing the tricorder. "I repaired all your injuries an hour ago, but I should check and make sure things are going smoothly." He just smiled, watching her work over him.

"Forget about that," he said, "I'm fine. Let's get out of here."

She closed the tricorder and gave him a smile. "Normally, I would agree with you. However the Dr. has ordered us to stay here for observation for the next twenty-four hours and I'm inclined to agree with him."

"In that case," he said, pushing a button on the side of his bed to make it double in size, "come join me." She smiled and climbed up onto the bio-bed, snuggling down into his embrace and laying her head on his chest. He reveled at her warmth next to his as he kissed her forehead and pulled her closer. After several minutes of blissful silence Chakotay whispered, "Kathryn?"

"Mmmmm," she mumbled, nearly fast asleep.

"I love you." He saw her smile a little smile to herself before she whispered, "I love you to Chakotay." A few seconds later her deep breathing told him she was asleep.

…

"Well Admiral, Borg nanoprobes aside, you seem to be in excellent health. However, I'm confining you to quarters for the rest of the day," the Dr. said the next day as he was clearing Kathryn and Chakotay to go.

"Thank you Dr."

"And Admiral, next time you want alone time with the Captain all you have to do is ask. Don't deactivate me," he quipped, turning his tricorder to Chakotay.

"Alright Dr. I'm sorry," Kathryn said with a laugh, patting him on the shoulder.

"You're free to go too Captain. It seems like the Admiral adequately healed your injuries. Just stay in your quarters for the next twenty-four hours."

"Thank you Dr," Chakotay said, getting off the bed and wrapping Kathryn's arm through his as they exited the Sick Bay.

"And come in tomorrow for another checkup before resuming active duty," the Dr. called after them, as they turned out of sight.

Chakotay and Kathryn exchanged a glance and began laughing, "Good old Dr. Hasn't changed a bit," Kathryn commented.

"Always protective of his captain."

"Just like a certain first officer I know," she said, giving him a kiss on the cheek.

"Hey, my motives are completely different from the Dr.'s."

"And they are…" she coaxed, with a sly smile and arch look. Raising his eyebrows and giving her a mischievous grin, he wrapped his hands around her waist and pushed her into an empty corridor, running his hands through her hair and kissing her passionately.

"That I'm deeply and crazily in love with you," he whispered in her ear, causing her to smile and return his kiss.

"Not as much as I am with you," she replied kissing him back. A few minutes later, she linked her arm back through his and they continued on their way.

"The problem we have to figure out now is how to spend the day with each other when the Dr. has confined us to quarters," he commented a few minutes later.

"Oh that's easy," she said with a saucy smile, "He confined you to your quarters but he only confined me to the quarters area…he never specified a specific one."

"So my quarters it is," he said with a laugh.

…

"Now I want to hear the whole story. What happened?" Chakotay asked as they snuggled on the couch drinking coffee and hot chocolate.

"Well, I went to the Borg cube to try and prove we had nothing to worry about. Voyager was going back to the Delta Quadrant over my dead body…"

"Yes, I've heard that part. Skip to when I entered your alcove."

"Well, I had been the queen for several weeks by that point and it was…horrible," she recalled, shuddering at the memory. "My mind was still there, but it was suppressed by her mind and the Borg collective. As much as I tried to fight against her I just…couldn't." At this point she broke down in sobs. Chakotay had never seen Kathryn cry before, and it scared him. Pulling her close he stroked her hair and kissed her cheek, trying to comfort her.

"I assimilated so many people…hundreds of lives lost because of me…"

"That wasn't you Kathryn. That was some monster that used you in a horrible way, but it was not you. You are in no way responsible for those people's deaths."

"But if I hadn't gone to the cube…"

"Then somebody else would have." He tipped her chin up so she was looking directly at him, tears still streaming down her face. "You did nothing wrong Kathryn. No one blames you at all. The Borg are the monsters, not you." She simply nodded as he wiped away her tears and held her close.

"Can you finish the story or would you like to stop?" he asked hesitantly.

"I've gone this far. I might as well finish the rest. Let's see…when you walked in I was immediately on alert. I hadn't seen you in months…not since…" she trailed off, blushing.

"The night we spent together after you finally acknowledged your feelings for me," he finished with a smile, taking her hand. That had been one of the happiest nights of his life and he would never forget it.

"Yes. I was overjoyed to see you, and your presence and touch gave me strength. I knew if I was ever going to break free this was the time. However, that still wasn't enough. As you saw, I could break through for several moments but then she came back. I had the horror of watching her hurt you. That's what really gave me strength…thinking of you and how I was causing you pain. When she tried to kill you, I was so scared I couldn't stop it; I couldn't bear to watch you die and know I had done it. However, I couldn't do anything."

Then she smiled for the first time in her whole recitation. "Then I heard you say you loved me. I don't know why, but that gave me the strength I needed. I think maybe I was dying for the opportunity to tell you I loved you too," she said, tracing his tattoo with her finger. "After that I was able to take control and stop her from killing you. I ran over to you and soon you were unconscious. I used your com to contact Voyager and Tom beamed us up to sickbay. You can probably guess the rest…the Dr. made sure I was severed from the collective for good, then I deactivated him and cared for you."

She leaned in and kissed him again, cupping his face in her hands. "Thank you," was all she said.

"For what?"

"For coming after me, for saving me…for loving me."

"Any time," he said smiling and taking both her hands in his. "I told you before Kathryn, I will always be here for you whether you like it or not. Your wants and needs will always come first. You are my life…I love you."

"And I love you Chakotay…more than anything."

"Then marry me." The words were out of his mouth before he could even think, and he could tell they surprised her. But once they were said he knew they made total sense. Almost losing her had taught him he never wanted to go through that again. If they were married, he wouldn't have to worry about that; they would be together forever. "I don't want to lose you again Kathryn. Please say you'll be my wife."

"Yes," she said in a small voice, barely a whisper. Than her face burst into the most radiant smile and she leaped on him, hugging him around the neck. "Oh yes!"

Smiling he pulled her to him and their lips met. All was right again with the universe.


End file.
